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• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• Error running cufflinks ( found spliced alignment without XS attribute) when use HISAT2 output Bam file
  Hello everyone, I have aligned my RNA seq paired read end by HISAT2 because Tophat is deprecate...
• Cuffdiff Fatal error: Matched on error
  Hello, I am doing my first RNA seq data analysis using galaxy. I have assembled my transcripts u...
• Bedgraph file problem
  I have received a set of BAM files generated from RNAseq (PE100) of the opossum, MonDom5. When ...
• genomic regions without reads
  Looking at custom BAM file with UCSC browser, I noticed that some reference genomic regions are n...
• Finding Snp Differences Between Datasets
  Hi, I am trying to find SNPs and/or indel variants that differ between two groups of samples. Th...
• Tophat Alignment Statistics?
  Hi, galaxy users How to get Tophat alignment statistics such as % of reads aligned to exon, intr...
• Compare 2 BAM files for covarage regions
  Hi, Is there a way to compare two BAM files for a difference in coverage and extract regions (giv...
• A Question Regarding Sequence Retrieval
  Dear Galaxy, I have the results for the sequence retrieval for Insulator ...
• Filtering list of regions to known refseq areas
  Hi, I have a set of Chip-seq-like data aligned to mm9, and have run SICER to peak call, thus gene...
• Cuffdiff crashing suddenly
  Hello, I'm running cuffdiff and this error comes up when it runs. Fatal error: Matched on e...
• how to merge multiple cufflink data in one file
  how to merge multiple cufflink data in one file. what i am expecting is rows will represent gene ...
• Re: Pilup File And Counting Reads In 200Bp Windows
  Hello Di, Once the data is in pile-up format, the read identifier is lost, so summarizing per-re...
• Count Reads Mapping To Introns, Extragenic Regions
  Hello everyone, I have some SAM/BAM files containing the alignments of some RNA-seq reads to hg1...
• How to find exonic and intronic regions from a set of coordinates?
  Hey, could anyone please help me with it? I have few coordinates of different chromosomes. I want...
• "View Details" Of Tophat Alignment
  Hi All, After I finshed Tophat alignment for RNA-seq, I took look at the details of parameters b...
• This job was terminated because it used more memory than it was allocated
  Hello, I have always encountered such problem "This job was terminated because it used more memo...